Load libraries and set the working diretory where the dataset_clean.Rds data is.
library(Seurat)
## Attaching SeuratObject
library(cowplot)
setwd("~/google_drive/ImmgenT/workshop1/")
sc <- readRDS('dataset_clean.Rds')
Structure of sc (Seurat Object) * Contains RNA data and ADT data (each a seperate assay) * Contains UMAP coordinates for both RNA and Protein Data * Contains following metadata for each cell: sample of origin, RNA cluster #, Protein cluster #, Hashtag identity
Similar to Rosetta, we can generate umaps for each of our metadata on both RNA and Protein level
Example: Plot UMAP RNA + color by sample
Idents(sc) <- "sample_name"
DimPlot(sc,reduction = "umap_rna")
Example 2: Plot UMAP Protein + color by sample
Idents(sc) <- "sample_name"
DimPlot(sc,reduction = "umap_adt")
Plot Cd4 RNA
DefaultAssay(object = sc) <- "RNA"
FeaturePlot(sc, features = 'Cd4', reduction = "umap_rna")
Plot CD4 protein
DefaultAssay(object = sc) <- "ADT"
FeaturePlot(sc, features = 'CD4', reduction = "umap_adt")
Plot Cd4 RNA x samples
DefaultAssay(object = sc) <- "RNA"
p <- FeaturePlot(sc, features = 'Cd4', reduction = "umap_rna", split.by = "sample_name", combine = F)
plot_grid(plotlist = p, ncol=2, label_size = 14)
## Warning: Removed 149 rows containing missing values (`geom_point()`).
## Removed 149 rows containing missing values (`geom_point()`).
## Removed 149 rows containing missing values (`geom_point()`).
## Removed 149 rows containing missing values (`geom_point()`).
## Removed 149 rows containing missing values (`geom_point()`).
## Removed 149 rows containing missing values (`geom_point()`).
## Removed 149 rows containing missing values (`geom_point()`).
## Removed 149 rows containing missing values (`geom_point()`).
## Removed 149 rows containing missing values (`geom_point()`).
## Removed 149 rows containing missing values (`geom_point()`).
Plot CD4 protein x samples
DefaultAssay(object = sc) <- "ADT"
p2 <- FeaturePlot(sc, features = 'CD4', reduction = "umap_adt", split.by = "sample_name", combine = F)
plot_grid(plotlist = p2, ncol=2, label_size = 14)
## Warning: Removed 149 rows containing missing values (`geom_point()`).
## Removed 149 rows containing missing values (`geom_point()`).
## Removed 149 rows containing missing values (`geom_point()`).
## Removed 149 rows containing missing values (`geom_point()`).
## Removed 149 rows containing missing values (`geom_point()`).
## Removed 149 rows containing missing values (`geom_point()`).
## Removed 149 rows containing missing values (`geom_point()`).
## Removed 149 rows containing missing values (`geom_point()`).
## Removed 149 rows containing missing values (`geom_point()`).
## Removed 149 rows containing missing values (`geom_point()`).